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Working with Workflows in PEITHO: Import, Export, and Execution

peitho_workflow_basics.Rmd

Introduction

This vignette demonstrates how to use the PEITHO package to manage, export, import, and execute workflows. The workflow system in PEITHO allows you to define a sequence of steps (such as data fetching, processing, or analysis), save and share workflows as zip files, and re-import or modify them for further use. This guide is aimed at users with basic R knowledge, but no advanced R expertise is required.

Prerequisites

  • Install the PEITHO package from GitHub if not already installed:

    devtools::install_github("Pandora-IsoMemo/PEITHO")

  • Load the package:

Loading the Example Workflow

You can create a workflow object from your own files by specifying a path, or use the example workflow included with PEITHO by passing an empty string as the path:

my_wf <- new_workflow(workflow_file_paths = workflow_file_paths(path = ""))
## INFO [2026-04-13 08:55:04] Creating empty results.json file.

Exporting a Workflow as a Zip File

You can export the current workflow setup (all relevant files) as a zip archive (here with the .peitho extension):

zipfile_path <- "./examples/my_workflow.peitho"
save_as_zip(my_wf, file = zipfile_path)
## INFO [2026-04-13 08:55:05] Creating directory './examples' for saving zip file.

Running a Workflow

To execute the workflow, use the run() function. You can specify which steps to run (e.g., from step 1 to 5):

my_run_1 <- run(my_wf, from = 1, to = 5)
## INFO [2026-04-13 08:55:05] Running step 1 of 5
## INFO [2026-04-13 08:55:05] Parsing arguments for command simple_split
## INFO [2026-04-13 08:55:05]   Command 'simple_split': 3 results
## INFO [2026-04-13 08:55:05] Running step 2 of 5
## INFO [2026-04-13 08:55:05] Parsing arguments for command fetch_WebText
## INFO [2026-04-13 08:55:06]   3 loop iterations for command 'fetch_WebText':
## INFO [2026-04-13 08:55:06]      3 single results.
## INFO [2026-04-13 08:55:06] Running step 3 of 5
## INFO [2026-04-13 08:55:06] Parsing arguments for command paste
## WARN [2026-04-13 08:55:06] WARNING! Detected list argument(s) for command 'paste', but 'loop' is set to 'no'.
## INFO [2026-04-13 08:55:06]   Command 'paste': single result
## INFO [2026-04-13 08:55:06] Running step 4 of 5
## INFO [2026-04-13 08:55:06] Parsing arguments for command gsub
## INFO [2026-04-13 08:55:06]   Command 'gsub': single result
## INFO [2026-04-13 08:55:06] Running step 5 of 5
## INFO [2026-04-13 08:55:06] Parsing arguments for command simple_split
## INFO [2026-04-13 08:55:06]   Command 'simple_split': 44271 results

After running, you can inspect the results:

length(my_run_1$state$last_result)
## [1] 44271
PEITHO:::trunc(my_run_1$state$last_result, n_char = 100)
## [1] "Toggl, \n th, \n tabl, \n of cont, \nnts Roman Empir, \n... (44266 more items)"

Importing and Modifying a Workflow from a Zip File

To import a workflow from a zip file, first define the directory where the workflow files will be extracted. You may also modify the workflow steps (for example, by editing commands.json or inputs.json in the extracted folder) before running it.

zipfile_path <- "./examples/my_workflow.peitho"

my_wf_imported <- PEITHO::import_workflow(
  zipfile = zipfile_path,
  extract_dir = "./examples/peitho_import"
)

You can now run the imported (and possibly modified) workflow and inspect the results as before:

my_run_2 <- run(my_wf_imported, from = 1, to = 4)
## INFO [2026-04-13 08:55:06] Running step 1 of 4
## INFO [2026-04-13 08:55:06] Parsing arguments for command simple_split
## INFO [2026-04-13 08:55:07]   Command 'simple_split': 3 results
## INFO [2026-04-13 08:55:07] Running step 2 of 4
## INFO [2026-04-13 08:55:07] Parsing arguments for command fetch_WebText
## INFO [2026-04-13 08:55:08]   3 loop iterations for command 'fetch_WebText':
## INFO [2026-04-13 08:55:08]      3 single results.
## INFO [2026-04-13 08:55:08] Running step 3 of 4
## INFO [2026-04-13 08:55:08] Parsing arguments for command paste
## WARN [2026-04-13 08:55:08] WARNING! Detected list argument(s) for command 'paste', but 'loop' is set to 'no'.
## INFO [2026-04-13 08:55:08]   Command 'paste': single result
## INFO [2026-04-13 08:55:08] Running step 4 of 4
## INFO [2026-04-13 08:55:08] Parsing arguments for command gsub
## INFO [2026-04-13 08:55:08]   Command 'gsub': single result
length(my_run_2$state$last_result)
## [1] 1
PEITHO:::trunc(my_run_2$state$last_result, n_char = 100)
## [1] "TogglHALLO thHALLO tablHALLO of contHALLOnts Roman EmpirHALLO 189 languagHALLOs abstract:Q2277 Acèh  ..."

Summary

PEITHO’s workflow system allows you to:

  • Load and execute multi-step workflows from configuration files
  • Export workflows as zip files for sharing or backup
  • Import and modify workflows from zip files
  • Inspect and print results from workflow execution

This makes it easy to share, reuse, and adapt complex analysis pipelines in a reproducible way.